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Yorodumi- PDB-1lcu: Polylysine Induces an Antiparallel Actin Dimer that Nucleates Fil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lcu | ||||||
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Title | Polylysine Induces an Antiparallel Actin Dimer that Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution | ||||||
Components | Actin, alpha skeletal muscle | ||||||
Keywords | CONTRACTILE PROTEIN / Structural protein / Muscle protein | ||||||
Function / homology | Function and homology information cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly ...cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Bubb, M.R. / Govindasamy, L. / Yarmola, E.G. / Vorobiev, S.M. / Almo, S.C. / Somasundaram, T. / Chapman, M.S. / Agbandje-Mckenna, M. / Mckenna, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Polylysine induces an antiparallel actin dimer that nucleates filament assembly: crystal structure at 3.5-A resolution. Authors: Bubb, M.R. / Govindasamy, L. / Yarmola, E.G. / Vorobiev, S.M. / Almo, S.C. / Somasundaram, T. / Chapman, M.S. / Agbandje-Mckenna, M. / Mckenna, R. #1: Journal: J.Biol.Chem. / Year: 2000 Title: Effects of Jasplakinolide on the Kinetics of Actin Polymerization. AN EXPLANATION FOR CERTAIN IN VIVO OBSERVATIONS Authors: Bubb, M.R. / Spector, I. / Beyer, B.B. / Fosen, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lcu.cif.gz | 164.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lcu.ent.gz | 126.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lcu_validation.pdf.gz | 665.7 KB | Display | wwPDB validaton report |
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Full document | 1lcu_full_validation.pdf.gz | 712.9 KB | Display | |
Data in XML | 1lcu_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 1lcu_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lcu ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lcu | HTTPS FTP |
-Related structure data
Related structure data | 1ijjC 1esvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41344.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 |
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-Non-polymers , 5 types, 95 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 8 |
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-Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.33 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium sulfate, MgCl2, Imidazole, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion / pH: 6.7 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 4, 2000 / Details: OSMIC MIRROR |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→30 Å / Num. obs: 15407 / % possible obs: 88.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.115 |
Reflection shell | Highest resolution: 3.5 Å / Rmerge(I) obs: 0.115 / Num. unique all: 15407 / % possible all: 88.8 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 101490 |
Reflection shell | *PLUS Rmerge(I) obs: 0.249 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ESV Resolution: 3.5→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Brunger & Adams
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.5→30 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 3.5 Å
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor all: 0.196 / Rfactor obs: 0.193 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.193 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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